HEADER APOPTOSIS/INHIBITOR 13-DEC-12 4IEH
TITLE CRYSTAL STRUCTURE OF HUMAN BCL-2 IN COMPLEX WITH A SMALL MOLECULE
TITLE 2 INHIBITOR TARGETING BCL-2 BH3 DOMAIN INTERACTIONS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1 CHIMERA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SEE REMARK 999;
COMPND 5 SYNONYM: BCL2-L-1, APOPTOSIS REGULATOR BCL-X;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: BCL2, BCL2L, BCL2L1, BCLX;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PROTEIN-PROTEIN INTERACTION, ALPHA HELICAL, PRO-APOPTOSIS, CYTOCHROME
KEYWDS 2 C RELEASE, CASPASE ACTIVATION, BIM, BAK, BAD, PUMA, APOPTOSIS-
KEYWDS 3 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR X.XIE,R.KULATHILA
REVDAT 3 26-JUL-17 4IEH 1 SOURCE REMARK
REVDAT 2 24-SEP-14 4IEH 1 JRNL
REVDAT 1 10-JUL-13 4IEH 0
JRNL AUTH B.B.TOURE,K.MILLER-MOSLIN,N.YUSUFF,L.PEREZ,M.DORE,C.JOUD,
JRNL AUTH 2 W.MICHAEL,L.DIPIETRO,S.VAN DER PLAS,M.MCEWAN,F.LENOIR,M.HOE,
JRNL AUTH 3 R.KARKI,C.SPRINGER,J.SULLIVAN,K.LEVINE,C.FIORILLA,X.XIE,
JRNL AUTH 4 R.KULATHILA,K.HERLIHY,D.PORTER,M.VISSER
JRNL TITL THE ROLE OF THE ACIDITY OF N-HETEROARYL SULFONAMIDES AS
JRNL TITL 2 INHIBITORS OF BCL-2 FAMILY PROTEIN-PROTEIN INTERACTIONS.
JRNL REF ACS MED CHEM LETT V. 4 186 2013
JRNL REFN ISSN 1948-5875
JRNL PMID 24900652
JRNL DOI 10.1021/ML300321D
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.74
REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 15959
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.179
REMARK 3 FREE R VALUE : 0.218
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 798
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 45.7512 - 3.8154 0.99 2675 141 0.1840 0.2318
REMARK 3 2 3.8154 - 3.0285 1.00 2544 134 0.1579 0.1876
REMARK 3 3 3.0285 - 2.6458 1.00 2512 132 0.1740 0.1893
REMARK 3 4 2.6458 - 2.4039 1.00 2494 132 0.1750 0.2113
REMARK 3 5 2.4039 - 2.2316 1.00 2482 130 0.1803 0.2638
REMARK 3 6 2.2316 - 2.1000 1.00 2454 129 0.2018 0.2528
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.32
REMARK 3 B_SOL : 46.18
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.490
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 32.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.71990
REMARK 3 B22 (A**2) : -3.71990
REMARK 3 B33 (A**2) : 7.43980
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.006 1261
REMARK 3 ANGLE : 0.980 1713
REMARK 3 CHIRALITY : 0.061 168
REMARK 3 PLANARITY : 0.006 216
REMARK 3 DIHEDRAL : 22.356 442
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4IEH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-12.
REMARK 100 THE DEPOSITION ID IS D_1000076650.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-JUN-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15960
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 48.100
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 7.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.09400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 7.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.46800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASES
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M SUCCINIC ACID, 0.25 M SODIUM
REMARK 280 MALONATE, 12% PEG3350, 0.1 M TRIS-HCL, PH 8.6, VAPOR DIFFUSION,
REMARK 280 TEMPERATURE 277.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.10250
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.76450
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.76450
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.15375
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.76450
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.76450
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.05125
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.76450
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.76450
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.15375
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.76450
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.76450
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.05125
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.10250
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 ALA A 2
REMARK 465 HIS A 3
REMARK 465 ALA A 4
REMARK 465 GLY A 5
REMARK 465 ARG A 6
REMARK 465 THR A 7
REMARK 465 GLY A 8
REMARK 465 ALA A 32
REMARK 465 GLY A 33
REMARK 465 ASP A 34
REMARK 465 ASP A 35
REMARK 465 VAL A 36
REMARK 465 GLU A 37
REMARK 465 GLU A 38
REMARK 465 ASN A 39
REMARK 465 ARG A 40
REMARK 465 THR A 41
REMARK 465 GLU A 42
REMARK 465 ALA A 43
REMARK 465 PRO A 44
REMARK 465 GLU A 45
REMARK 465 GLY A 46
REMARK 465 THR A 47
REMARK 465 GLU A 48
REMARK 465 SER A 164
REMARK 465 MET A 165
REMARK 465 ARG A 166
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1E9 A 201
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 PROTEIN IS A CHIMERA COMPRISING RESIDUES 1-34 OF BCL-2 (UNP P10415),
REMARK 999 RESIDUES 29-44 OF BCL-X (UNP Q07817), AND RESIDUES 92-207 OF BCL-2
REMARK 999 (UNP P10415).
DBREF 4IEH A 1 34 UNP P10415 BCL2_HUMAN 1 34
DBREF 4IEH A 35 50 UNP Q07817 B2CL1_HUMAN 29 44
DBREF 4IEH A 51 166 UNP P10415 BCL2_HUMAN 92 207
SEQADV 4IEH GLY A -2 UNP P10415 CLONING ARTIFACT
SEQADV 4IEH SER A -1 UNP P10415 CLONING ARTIFACT
SEQADV 4IEH HIS A 0 UNP P10415 CLONING ARTIFACT
SEQRES 1 A 169 GLY SER HIS MET ALA HIS ALA GLY ARG THR GLY TYR ASP
SEQRES 2 A 169 ASN ARG GLU ILE VAL MET LYS TYR ILE HIS TYR LYS LEU
SEQRES 3 A 169 SER GLN ARG GLY TYR GLU TRP ASP ALA GLY ASP ASP VAL
SEQRES 4 A 169 GLU GLU ASN ARG THR GLU ALA PRO GLU GLY THR GLU SER
SEQRES 5 A 169 GLU VAL VAL HIS LEU THR LEU ARG GLN ALA GLY ASP ASP
SEQRES 6 A 169 PHE SER ARG ARG TYR ARG ARG ASP PHE ALA GLU MET SER
SEQRES 7 A 169 SER GLN LEU HIS LEU THR PRO PHE THR ALA ARG GLY ARG
SEQRES 8 A 169 PHE ALA THR VAL VAL GLU GLU LEU PHE ARG ASP GLY VAL
SEQRES 9 A 169 ASN TRP GLY ARG ILE VAL ALA PHE PHE GLU PHE GLY GLY
SEQRES 10 A 169 VAL MET CYS VAL GLU SER VAL ASN ARG GLU MET SER PRO
SEQRES 11 A 169 LEU VAL ASP ASN ILE ALA LEU TRP MET THR GLU TYR LEU
SEQRES 12 A 169 ASN ARG HIS LEU HIS THR TRP ILE GLN ASP ASN GLY GLY
SEQRES 13 A 169 TRP ASP ALA PHE VAL GLU LEU TYR GLY PRO SER MET ARG
HET 1E9 A 201 59
HETNAM 1E9 N-(6-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-
HETNAM 2 1E9 YL}-1,1-DIOXIDO-1,2-BENZOTHIAZOL-3-YL)-4-{[(2R)-4-
HETNAM 3 1E9 (DIMETHYLAMINO)-1-(PHENYLSULFANYL)BUTAN-2-YL]AMINO}-3-
HETNAM 4 1E9 NITROBENZENESULFONAMIDE
FORMUL 2 1E9 C42 H44 CL N7 O6 S3
FORMUL 3 HOH *184(H2 O)
HELIX 1 1 ASP A 10 ARG A 26 1 17
HELIX 2 2 GLU A 50 TYR A 67 1 18
HELIX 3 3 TYR A 67 SER A 75 1 9
HELIX 4 4 SER A 76 LEU A 78 5 3
HELIX 5 5 THR A 84 PHE A 97 1 14
HELIX 6 6 ASN A 102 ARG A 123 1 22
HELIX 7 7 PRO A 127 LEU A 144 1 18
HELIX 8 8 LEU A 144 ASN A 151 1 8
HELIX 9 9 GLY A 152 GLY A 162 1 11
SITE 1 AC1 20 ALA A 59 ASP A 62 ARG A 66 TYR A 67
SITE 2 AC1 20 PHE A 71 MET A 74 GLY A 104 ARG A 105
SITE 3 AC1 20 VAL A 107 ALA A 108 GLU A 124 MET A 125
SITE 4 AC1 20 SER A 126 PHE A 157 TYR A 161 HOH A 319
SITE 5 AC1 20 HOH A 360 HOH A 366 HOH A 367 HOH A 436
CRYST1 73.529 73.529 96.205 90.00 90.00 90.00 P 43 21 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.013600 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013600 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010394 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
